Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Trp53

Cell type

Cell type Class
Lung
Cell type
Alveolar organoids
NA
NA

Attributes by original data submitter

Sample

source_name
Alveolar organoids
cell type
Alveolar organoids
genotype
Wild-type
treatment
DMSO, 24h
chip antibody
p53 (D2H9O) Rabbit mAb, CST #32532
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM7286002
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in a PBS (-) solution containing 1 % formaldehyde and 2 mM DSG for 10 min. ChIP was performed as previously described (Kadota et al, 2017) except that, RIPA buffer was used instead of LB3 lysis buffer at permeabilization and sonication steps. Chromatin lysate from 1-5 × 10^7 organoid cells was prepared using the Covaris S220 sonicator. Illumina compatible libraries were prepared from 20 ng of input DNA or the 2-4 ng ChIP DNA after size selection for 50-400 bp DNA fragments by AMPure XP beads, using the KAPA LTP Library Preparation kit and TruSeq DNA UD Indexes.

Sequencing Platform

instrument_model
NextSeq 2000

mm10

Number of total reads
30504139
Reads aligned (%)
88.8
Duplicates removed (%)
24.4
Number of peaks
21779 (qval < 1E-05)

mm9

Number of total reads
30504139
Reads aligned (%)
88.7
Duplicates removed (%)
24.5
Number of peaks
21746 (qval < 1E-05)

Base call quality data from DBCLS SRA